> Sequence data read successfully
> Organism codon frequency file read successfully
> Mode selected: (p)rotein optimization
> Files & libraries read successfully
> ------------------------------------------
> Organism used is ecoliK12
> All sequences are OK (nt/AA)
> ====================================================================================
> Protein sequence optimization starting...
> NOTE: For protein optimization, the sequences file can contain either nucleotide or single letter
	amino acid sequences.  Each sequence should be on a separate line, blank newline entries in the 
	file will result in a read error.  The file should contain no other characters than the ones for a
	sequence.  You can have the protein sequences in either amino acid or nucleotide sequence, and 
	sequences in the file are not limited to only one format.  The program will automatically translate
	DNA and/or Protein sequences into a preliminary optimized DNA sequence, which will subsequently be
	further optimized. If your file is not formatted as such, please press [Ctrl]-C to stop the program 
	and reformat your file.
> ==========================================
> Sequence 0 is (DNA form):
	gcgcagcaggtgtatgcgaaaccgacctataaacagtatcgcaactatctgccggataaatggatgaaaggcaacgcgtggattaacgtgatgagcaaaggcgcgtggcgccagtttccgtgcccgatgtgccgcgtgccgaaaggcttttttccgaactatgtgatgtggaacccgggc
  Translation (initial): 
	aqqvyakptykqyrnylpdkwmkgnawinvmskgawrqfpcpmcrvpkgffpnyvmwnpg
  Restriction Sites found at following indices to be removed: 
	['mlui', 'acgcgt', [73]]
	['smai', 'cccggg', [173]]
	['tspmi', 'cccggg', [173]]
	['xmai', 'cccggg', [173]]
  Codon optimized and and (-) restriction site sequence:
	gcgcagcaggtgtatgcgaaaccgacctataaacagtatcgcaactatctgccggataaatggatgaaaggcaatgcgtggattaacgtgatgagcaaaggcgcgtggcgccagtttccgtgcccgatgtgccgcgtgccgaaaggcttttttccgaactatgtgatgtggaatccgggc
  Translation (verification): -good optimization
	aqqvyakptykqyrnylpdkwmkgnawinvmskgawrqfpcpmcrvpkgffpnyvmwnpg
  Optimization complete
> ==========================================
> Sequence 1 is (DNA form):
	ggcctgagcgcgcgcagctttgatggcctggtgccgacccgccgccatagctttcgccgcattattcgcggccagtaacagccgaccagccgcgtgctgccgaaccgcagcacccgctaa
  Translation (initial): 
	glsarsfdglvptrrhsfrriirgq*qptsrvlpnrstr*
  No restriction sites found, only codon optimization needed
  Codon optimized and and (-) restriction site sequence:
	ggcctgagcgcgcgcagctttgatggcctggtgccgacccgccgccatagctttcgccgcattattcgcggccagtaacagccgaccagccgcgtgctgccgaaccgcagcacccgctaa
  Translation (verification): -good optimization
	glsarsfdglvptrrhsfrriirgq*qptsrvlpnrstr*
  Optimization complete
> ==========================================
> Sequence 2 is (DNA form):
	gaaatgaaaaccgtgattctgaaatgccgctgcgaactgcgctgcaccgcgaaagatattaacaaatgccgcccggatccggaaatgatgcatcgcattccgtgcgtggtgccggaatattgcgcgatg
  Translation (initial): 
	emktvilkcrcelrctakdinkcrpdpemmhripcvvpeycam
  Restriction Sites found at following indices to be removed: 
	['bamhi', 'ggatcc', [74]]
	['nsii', 'atgcat', [87]]
  Codon optimized and and (-) restriction site sequence:
	gaaatgaaaaccgtgattctgaaatgccgctgcgaactgcgctgcaccgcgaaagatattaacaaatgccgcccggacccggaaatgatgcaccgcattccgtgcgtggtgccggaatattgcgcgatg
  Translation (verification): -good optimization
	emktvilkcrcelrctakdinkcrpdpemmhripcvvpeycam
  Optimization complete
> ==========================================
> Sequence 3 is (DNA form):
	cgcgaagtgtgcattttttggaaccatgaagtgatgatggcgtgcaacagcccgcgcgtgtataaattttggagcgcgcagacctgctgcgatattaccatttttgatattattggccattgcgaacgcaccgaaatttattttattctgatggattttcgcgaaccggtgatgaccgcg
  Translation (initial): 
	revcifwnhevmmacnsprvykfwsaqtccditifdiighcerteiyfilmdfrepvmta
  Restriction Sites found at following indices to be removed: 
	['agei', 'accggt', [164]]
  Codon optimized and and (-) restriction site sequence:
	cgcgaagtgtgcattttttggaaccatgaagtgatgatggcgtgcaacagcccgcgcgtgtataaattttggagcgcgcagacctgctgcgatattaccatttttgatattattggccattgcgaacgcaccgaaatttattttattctgatggattttcgcgagccggtgatgaccgcg
  Translation (verification): -good optimization
	revcifwnhevmmacnsprvykfwsaqtccditifdiighcerteiyfilmdfrepvmta
  Optimization complete
> ==========================================
> Sequence 4 is (DNA form):
	agcgaaaccccgaccccgggcgtgaactggttttgcctggatgattgggtgaccaaatataaactgctgcagagcaccctgattcaggtgtattgggcgtgctttgcgcagtggaaaaacaaaattcgctggatgaaactgcagaaacagaaatttatgcgcgaagcgtgggcgctggtg
  Translation (initial): 
	setptpgvnwfclddwvtkykllqstliqvywacfaqwknkirwmklqkqkfmreawalv
  Restriction Sites found at following indices to be removed: 
	['psti', 'ctgcag', [66, 138]]
	['smai', 'cccggg', [14]]
	['tspmi', 'cccggg', [14]]
	['xmai', 'cccggg', [14]]
  Codon optimized and and (-) restriction site sequence:
	agcgaaaccccgacgccgggcgtgaactggttttgcctggatgattgggtgaccaaatataaactgttacagagcaccctgattcaggtgtattgggcgtgctttgcgcagtggaaaaacaaaattcgctggatgaaattacagaaacagaaatttatgcgcgaagcgtgggcgctggtg
  Translation (verification): -good optimization
	setptpgvnwfclddwvtkykllqstliqvywacfaqwknkirwmklqkqkfmreawalv
  Optimization complete
> ==========================================
> Sequence 5 is (DNA form):
	agcagcccgcgcattctgtttgcggatccgcagtggccggtggatacccgcccgccgcgctgcagcgtgaccggcacc
  Translation (initial): 
	ssprilfadpqwpvdtrpprcsvtgt
  Restriction Sites found at following indices to be removed: 
	['bamhi', 'ggatcc', [23]]
	['psti', 'ctgcag', [59]]
  Codon optimized and and (-) restriction site sequence:
	agcagcccgcgcattctgtttgccgatccgcagtggccggtggatacccgcccgccgcgttgcagcgtgaccggcacc
  Translation (verification): -good optimization
	ssprilfadpqwpvdtrpprcsvtgt
  Optimization complete
> ==========================================
> Sequence 6 is (DNA form):
	gtgacccagattccgggctgcctggatagcggcaaacatattcagtgcgaagtgtatgattattggctggataaaccggcgtttgtgtataaccgctggcatatggtgcagcgcgtgctgtgccagcagccggaatatgtggcgaaaagccagacctgcgtgcattttttttgctgccgc
  Translation (initial): 
	vtqipgcldsgkhiqcevydywldkpafvynrwhmvqrvlcqqpeyvaksqtcvhffccr
  Restriction Sites found at following indices to be removed: 
	['ndei', 'catatg', [99]]
  Codon optimized and and (-) restriction site sequence:
	gtgacccagattccgggctgcctggatagcggcaaacatattcagtgcgaagtgtatgattattggctggataaaccggcgtttgtgtataaccgctggcacatggtgcagcgcgtgctgtgccagcagccggaatatgtggcgaaaagccagacctgcgtgcattttttttgctgccgc
  Translation (verification): -good optimization
	vtqipgcldsgkhiqcevydywldkpafvynrwhmvqrvlcqqpeyvaksqtcvhffccr
  Optimization complete
> ==========================================
> Sequence 7 is (DNA form):
	ccgcgcacccgccgccatgcgatggaacgcccgtaactgcgccaggcgattaaaggcaacgtgtgcattacccagaaaaaccgcaaaattggcgaataaatttttagcctgtgcattgaagaatggccgcgcggcggcatgcgccatgcgagc
  Translation (initial): 
	prtrrhamerp*lrqaikgnvcitqknrkige*ifslcieewprggmrhas
  Restriction Sites found at following indices to be removed: 
	['sphi', 'gcatgc', [136]]
  Codon optimized and and (-) restriction site sequence:
	ccgcgcacccgccgccatgcgatggaacgcccgtaactgcgccaggcgattaaaggcaacgtgtgcattacccagaaaaaccgcaaaattggcgaataaatttttagcctgtgcattgaagaatggccgcgcggcggtatgcgccatgcgagc
  Translation (verification): -good optimization
	prtrrhamerp*lrqaikgnvcitqknrkige*ifslcieewprggmrhas
  Optimization complete
> ==========================================
> Sequence 8 is (DNA form):
	attatgcagaaaccgtgcgatattgataacgaactgaaaaaaattctgagcaaatttattgaaaaccatgtgtttgatattccgcagcataacaaagtgagcaacgatcaggtgggccgctgctggatgttttgcgatcgcccggaacgccagacctttaacatgggcaacatgatgatg
  Translation (initial): 
	imqkpcdidnelkkilskfienhvfdipqhnkvsndqvgrcwmfcdrperqtfnmgnmmm
  Restriction Sites found at following indices to be removed: 
	['pvui', 'cgatcg', [134]]
  Codon optimized and and (-) restriction site sequence:
	attatgcagaaaccgtgcgatattgataacgaactgaaaaaaattctgagcaaatttattgaaaaccatgtgtttgatattccgcagcataacaaagtgagcaacgatcaggtgggccgctgctggatgttttgtgatcgcccggaacgccagacctttaacatgggcaacatgatgatg
  Translation (verification): -good optimization
	imqkpcdidnelkkilskfienhvfdipqhnkvsndqvgrcwmfcdrperqtfnmgnmmm
  Optimization complete
> ==========================================
> Sequence 9 is (DNA form):
	gtgtttgaagcgcagaaaccgccggtggcgtttctgaccgattgctatcagtggatgaccctgccgagctttgattatcaggtgacctatatgatgaacaacgatgattatgcgattaaa
  Translation (initial): 
	vfeaqkppvafltdcyqwmtlpsfdyqvtymmnnddyaik
  No restriction sites found, only codon optimization needed
  Codon optimized and and (-) restriction site sequence:
	gtgtttgaagcgcagaaaccgccggtggcgtttctgaccgattgctatcagtggatgaccctgccgagctttgattatcaggtgacctatatgatgaacaacgatgattatgcgattaaa
  Translation (verification): -good optimization
	vfeaqkppvafltdcyqwmtlpsfdyqvtymmnnddyaik
  Optimization complete
> ==========================================
> Sequence 10 is (DNA form):
	tatagcgaaagc
  Translation (initial): 
	yses
  No restriction sites found, only codon optimization needed
  Codon optimized and and (-) restriction site sequence:
	tatagcgaaagc
  Translation (verification): -good optimization
	yses
  Optimization complete
> ==========================================
> QuitFlush completed, Process Completed.
